Fix bug when number of GFFs is large

SionBayliss / PIRATE

A toolbox for pangenome analysis and threshold evaluation.

GNU General Public License v3.0

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Fix bug when number of GFFs is large #72

Closed dorbarker closed 2 years ago

dorbarker commented 3 years ago

When the number of GFFs is large (in my case, >30000), PIRATE fails when "Standardising and checking input files". This happens because the number of files can exceed the maximum argument number for the external shell commands PIRATE uses at this step. This patch avoids this issue by loading the GFF file paths into a perl array, which then sends chunks equal in size to $threads to parallel instead of getting the file list with ls.

SionBayliss commented 2 years ago

Hi Dillon,

Thanks for your work on this. Much appreciated!

Cheers, Sion